Structure of PDB 4d6s Chain A Binding Site BS02

Receptor Information
>4d6s Chain A (length=327) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKAR
ETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKY
QTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTI
QDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPK
TWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIP
FNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQC
SCGEARVTFSMDAFVRILQPERYDLWK
Ligand information
Ligand IDDMD
InChIInChI=1S/C9H10N2/c1-6-3-8-9(4-7(6)2)11-5-10-8/h3-5H,1-2H3,(H,10,11)
InChIKeyLJUQGASMPRMWIW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04n2c1cc(c(cc1nc2)C)C
CACTVS 3.341Cc1cc2[nH]cnc2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)nc[nH]2
FormulaC9 H10 N2
Name5,6-DIMETHYLBENZIMIDAZOLE
ChEMBLCHEMBL351132
DrugBankDB02591
ZINCZINC000000388593
PDB chain4d6s Chain A Residue 1340 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4d6s Crystal Structure of Human Jmjd2D in Complex with N-Oxalylglycine and Bound 5,6- Dimethylbenzimidazole
Resolution1.4 Å
Binding residue
(original residue number in PDB)		Q221 Y277
Binding residue
(residue number reindexed from 1)		Q211 Y267
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G174 Y181 H192 E194 H280 A292
Catalytic site (residue number reindexed from 1) G164 Y171 H182 E184 H270 A282
Enzyme Commision number 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.
External links
PDB RCSB:4d6s, PDBe:4d6s, PDBj:4d6s
PDBsum4d6s
PubMed
UniProtQ6B0I6|KDM4D_HUMAN Lysine-specific demethylase 4D (Gene Name=KDM4D)

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